Study of the kinetics of apolipoprotein metabolism can provide important information regarding the regulation of lipid transport in humans. At present the majority of these studies are performed by radiolabeling the apolipoproteins. Methods have been developed for the determination of the isotope enrichment of several amino acids in plasma by chemical ionization mass spectrometry. The kinetics of all the proteins in the plasma can now be studied by using stable isotopes, thus avoiding the use of radioactive materials.A bolus injection, or constant infusion of a stable isotope labeled amino acid will result in endogenous labeling of all the apolipoproteins. Chemical ionization mass spectrometry using isobutane as the reagent gas has been employed to compare the levels of both 15N and 13C labeled amino acids in apolipoproteins, using their heptafluorobutyril isobutyl esters. The results obtained indicates that sufficient labeling of all proteins can be achieved by bolus injection, or constant infusion. Endogenous labeling of proteins avoids the potential for denaturing, or altering the conformation of the protein. All the proteins in the plasma will undergo labeling and any individual protein can be isolated and its metabolism studied. Using this technique we have determined the metabolic rates of various proteins from normal subjects as well as patients with different lipoprotein abnormalities, like A-I-Iowa, A-I-Tangier, and E-Harrisburg. The mutated proteins in A-I-Iowa and E-Harrisburg have been found to have a totally different metabolism than the corresponding normal proteins. On the other hand, A-I-Tangier patients were found to have extremely fast catabolism of a normal protein. The low levels of HDL and apoA-I were due to either metabolic defects of increased apoA-I catabolism or decreased apoA-I production. Direct comparison of the two methods (radiolabel vs stable isotope label) were also made in order to study the accuracy of each method. Our data suggest that the method of endogenous labeling provides kinetic parameters which correlate very closely with those obtained by exogenous labeling method.